1. Field of the Invention
This invention relates generally to the field of X-ray diffraction and, more specifically, to the processing of topped reflections in the data collected for determining the structure of a crystalline compound.
2. Description of the Related Art
Single-crystal X-ray diffraction (SC-XRD) is a method for determining the three-dimensional atomic structure of a crystalline compound. A single-crystal specimen of the compound is irradiated with monochromatic X-ray radiation from different directions, some of which is diffracted in specific patterns and detected by an X-ray detector. The structural information of the specimen is determined from the geometry and relative intensities of these diffraction patterns. The intensities are integrated from the pixels in the X-ray detector images.
A typical laboratory system 100 for performing single-crystal diffraction experiments consists of five components as shown in FIG. 1. The components include an X-ray source 102 that produces a primary X-ray beam 104 with the required radiation energy, focal spot size and intensity. X-ray optics 106 are provided to condition the primary X-ray beam 104 to a conditioned, or incident, beam 108 with the required wavelength, beam focus size, beam profile and divergence. A goniometer 110 is used to establish and manipulate geometric relationships between the incident X-ray beam 108, the crystal sample 112 and the X-ray sensor 114. The incident X-ray beam 108 strikes the crystal sample 112 and produces scattered X-rays 116 which are recorded in the sensor 114. A sample alignment and monitor assembly comprises a sample illuminator 118 that illuminates the sample 112 and a sample monitor 120, typically a video camera, which generates a video image of the sample to assist users in positioning the sample in the instrument center and monitoring the sample's state and position.
The goniometer 110 allows the crystal sample 112 to be rotated around several axes. Precise crystallography requires that the sample crystal 112 be aligned to the center of the goniometer 110 and maintained in that center when rotated around the goniometer rotational axes during data collection. During exposure, the sample (a single crystal of the compound of interest) is rotated in the X-ray beam 108 through a precise angular range with a precise angular velocity. The purpose of this rotation is to predictably bring Bragg reflections into constructive interference. At each rotational position, the sensor captures an image of the diffracted X-ray signals. The result of such an X-ray diffraction experiment is thus a set of 2D images whose pixels indicate the locations and the intensities of the individual reflections.
A crystalline compound has a continuous distribution of electrons. When incident X-rays hit the compound, they are diffracted with a specific diffraction pattern by the electrons. The diffracted X-rays create reflections in the 2D images captured by the detector 114. The diffraction pattern of the reflections is related to the density map of electrons of the compound by a Fourier Transform. Based on the location of the reflections within the set of 2D images, and based on the intensities of the pixels defining the reflections, a reciprocal sphere of data may be generated, with discrete reflections being positioned, one relative to the other, in the reciprocal sphere, the intensity of each reflection being a coefficient of the Fourier transform. The relative intensities of the reflections in turn yield information about the arrangement of the electrons in the crystal structure. Applying an inverse Fourier Transform to the 3D reciprocal sphere data provides the electron density map, which is in turn indicative of the structure of the crystalline compound.
FIG. 2 shows typical steps conducted during an X-ray diffraction experiment. The experiment typically starts with conducting a pre-experiment (step 200) to collect a few diffraction images, sufficient to determine the appropriate data collection parameters for the main experiment. Deciding on the proper data collection parameters to use in the main experiment will depend on the unit cell of the crystal sample, its mosaicity, the signal-to-noise ratio I/sigma(I), where sigma is the standard deviation) to achieve for a given resolution, the diffraction limit and the orientation matrix of the experiment set-up, which are all determined during the pre-scan experiment. The pre-experiment allows, for example, a determination of the optimized exposure time to use for each image captured by the detector in the main experiment. With slow acquisition speeds and long dead time of traditional diffraction systems, typically, only partial data is collected during the pre-experiment.
When conducting the main X-ray diffraction experiment (step 202), the exposure time of the X-ray detector is selected to allow detection of both stronger and weaker intensity reflections. However, even if the exposure time is optimized using information about the intensity distribution obtained during pre-experiment (step 200), stronger reflections will saturate some of the pixels of the detector during the main experiment. In other words, even with optimized parameters, some of the reflection signals will extend beyond the dynamic range of the X-ray detector, resulting in inaccurate data collected for these reflections. These reflections are often referred to as “topped” or “overload” reflections. The correct intensity of these topped signals cannot be recorded correctly and needs to be reconstructed from additional images. As such, known methods require that while conducting the main experiment, each image is verified in order to determine whether or not saturated pixels are present in an image (step 204).
Traditionally, the intensity data of saturated pixels was either discarded or a new image frame was captured during a second exposure, with higher scan speed and shorter exposure time, or with an attenuated X-ray beam (step 206). Both measures reduce the intensity of the signal, such that it falls in the dynamic range of the detector. The intensity of the pixels that had saturated in the original image is replaced with a scaled intensity of the pixels of the second exposure and a composite image is built based on the two images resulting from the first and second exposures (step 208). The conventional method is time-consuming since the images must be read and analyzed during the main experiment to determine whether saturated pixels are present or not. If saturated pixels are present, the goniometer must be stopped, the intensity of the beam needs to be attenuated and/or the exposure time must be reduced in order to capture a second image without any saturated pixels.
The result of the diffraction experiment is a set of many diffraction images (210) with pixels containing intensities of the reflections. The intensities of each reflection are then integrated, scaled, and normalized (steps 212, 214). The output data provide a location and intensity for each reflection in the reciprocal space (216). The output data can then be used to determine the electron density map of the sample by applying an inverse Fourier transform. The electron density map in turn allows one to determine the structure of the crystalline sample.